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Khaparkhuntikar K, Maji I, Gupta SK, Mahajan S, Aalhate M, Sriram A, Gupta U, Guru SK, Kulkarni P, Singh PK. Acalabrutinib as a novel hope for the treatment of breast and lung cancer: an in-silico proof of concept. J Biomol Struct Dyn 2024; 42:1469-1484. [PMID: 37272883 DOI: 10.1080/07391102.2023.2217923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 04/01/2023] [Indexed: 06/06/2023]
Abstract
Drug repurposing is proved to be a groundbreaking concept in the field of cancer research, accelerating the pace of de novo drug discovery by investigating the anti-cancer activity of the already approved drugs. On the other hand, it got highly benefitted from the advancement in the in-silico tools and techniques, which are used to build up the initial "proof of concept" based on the drug-target interaction. Acalabrutinib (ACL) is a well-known drug for the treatment of hematological malignancies. But, the therapeutic ability of ACL against solid tumors is still unexplored. Thereby, the activity of ACL on breast cancer and lung cancer was evaluated utilizing different computational methods. A series of proteins such as VEGFR1, ALK, BCL2, CXCR-4, mTOR, AKT, PI3K, HER-2, and Estrogen receptors were selected based on their involvement in the progression of the breast as well as lung cancer. A multi-level computational study starting from protein-ligand docking to molecular dynamic (MD) simulations were performed to detect the binding potential of ACL towards the selected proteins. Results of the study led to the identification of ACL as a ligand that showed a high docking score and binding energy with HER-2, mTOR, and VEGFR-1 successively. Whereas, the MD simulations study has also shown good docked complex stability of ACL with HER2 and VEGFR1. Our findings suggest that interaction with those receptors can lead to preventive action on both breast and lung cancer, thus it can be concluded that ACL could be a potential molecule for the same purpose.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kedar Khaparkhuntikar
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Indrani Maji
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Sunil Kumar Gupta
- Department of Bioinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Srushti Mahajan
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Mayur Aalhate
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Anitha Sriram
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Ujala Gupta
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Santosh Kumar Guru
- Department of Biological Science, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Prachi Kulkarni
- Department of Physiology, Shri B. M. Patil Medical College, Hospital & Research Centre BLDE (Deemed to be University), Vijayapura, Karnataka, India
| | - Pankaj Kumar Singh
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
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Passero M, Zhai T, Huang Z. Investigation of Potential Drug Targets for Cholesterol Regulation to Treat Alzheimer's Disease. Int J Environ Res Public Health 2023; 20:6217. [PMID: 37444065 PMCID: PMC10341567 DOI: 10.3390/ijerph20136217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/08/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023]
Abstract
Despite extensive research and seven approved drugs, the complex interplay of genes, proteins, and pathways in Alzheimer's disease remains a challenge. This implies the intricacies of the mechanism for Alzheimer's disease, which involves the interaction of hundreds of genes, proteins, and pathways. While the major hallmarks of Alzheimer's disease are the accumulation of amyloid plaques and tau protein tangles, excessive accumulation of cholesterol is reportedly correlated with Alzheimer's disease patients. In this work, protein-protein interaction analysis was conducted based upon the genes from a clinical database to identify the top protein targets with most data-indicated involvement in Alzheimer's disease, which include ABCA1, CYP46A1, BACE1, TREM2, GSK3B, and SREBP2. The reactions and pathways associated with these genes were thoroughly studied for their roles in regulating brain cholesterol biosynthesis, amyloid beta accumulation, and tau protein tangle formation. Existing clinical trials for each protein target were also investigated. The research indicated that the inhibition of SREBP2, BACE1, or GSK3B is beneficial to reduce cholesterol and amyloid beta accumulation, while the activation of ABCA1, CYP46A1, or TREM2 has similar effects. In this study, Sterol Regulatory Element-Binding Protein 2 (SREBP2) emerged as the primary protein target. SREBP2 serves a pivotal role in maintaining cholesterol balance, acting as a transcription factor that controls the expression of several enzymes pivotal for cholesterol biosynthesis. Novel studies suggest that SREBP2 performs a multifaceted role in Alzheimer's disease. The hyperactivity of SREBP2 may lead to heightened cholesterol biosynthesis, which suggested association with the pathogenesis of Alzheimer's disease. Lowering SREBP2 levels in an Alzheimer's disease mouse model results in reduced production of amyloid-beta, a major contributor to Alzheimer's disease progression. Moreover, its thoroughly analyzed crystal structure allows for computer-aided screening of potential inhibitors; SREBP2 is thus selected as a prospective drug target. While more protein targets can be added onto the list in the future, this work provides an overview of key proteins involved in the regulation of brain cholesterol biosynthesis that may be further investigated for Alzheimer's disease intervention.
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Affiliation(s)
| | | | - Zuyi Huang
- Department of Chemical Engineering, Villanova University, Villanova, PA 19085, USA
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Khalid A, Abdalla M, Saeed M, Ghayur MN, Kalauni SK, Albratty M, Alhazmi HA, Mesaik MA, Gilani AH, Ul-Haq Z. Sarcorucinine-D Inhibits Cholinesterases and Calcium Channels: Molecular Dynamics Simulation and In Vitro Mechanistic Investigations. Molecules 2022; 27:molecules27113361. [PMID: 35684298 PMCID: PMC9182202 DOI: 10.3390/molecules27113361] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 11/28/2022]
Abstract
Acetylcholinesterase (AChE) inhibitors and calcium channel blockers are considered effective therapies for Alzheimer’s disease. AChE plays an essential role in the nervous system by catalyzing the hydrolysis of the neurotransmitter acetylcholine. In this study, the inhibition of the enzyme AChE by Sarcorucinine-D, a pregnane type steroidal alkaloid, was investigated with experimental enzyme kinetics and molecular dynamics (MD) simulation techniques. Kinetics studies showed that Sarcorucinine-D inhibits two cholinesterases—AChE and butyrylcholinesterase (BChE)—noncompetitively, with Ki values of 103.3 and 4.66 µM, respectively. In silico ligand-protein docking and MD simulation studies conducted on AChE predicted that Sarcorucinine-D interacted via hydrophobic interactions and hydrogen bonds with the residues of the active-site gorge of AChE. Sarcorucinine-D was able to relax contractility concentration-dependently in the intestinal smooth muscles of jejunum obtained from rabbits. Not only was the spontaneous spasmogenicity inhibited, but it also suppressed K+-mediated spasmogenicity, indicating an effect via the inhibition of voltage-dependent Ca2+ channels. Sarcorucinine-D could be considered a potential lead molecule based on its properties as a noncompetitive AChE inhibitor and a Ca2+ channel blocker.
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Affiliation(s)
- Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia;
- Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, P.O. Box 2424, Khartoum 11111, Sudan
- Correspondence:
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Jinan 250012, China;
| | - Maria Saeed
- Dr. Panjwani Center for Molecular Medicine & Drug Research, University of Karachi, Karachi 75530, Pakistan; (M.S.); (Z.U.-H.)
| | - Muhammad Nabeel Ghayur
- Department of Biomedical Sciences, University of Pikeville, Pikeville, KY 41501, USA;
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan;
| | - Surya Kant Kalauni
- Central Department of Chemistry, Tribhuvan University, Kirtipur 44618, Nepal;
| | - Mohammed Albratty
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia;
| | - Hassan A. Alhazmi
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia;
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia;
| | - Mohammed Ahmed Mesaik
- Department of Medical Microbiology, Faculty of Medicine, University of Tabuk, Tabuk 71491, Saudi Arabia;
| | - Anwarul Hassan Gilani
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan;
- Department of Public Health and Nutrition, University of Haripur, Haripur 22620, Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine & Drug Research, University of Karachi, Karachi 75530, Pakistan; (M.S.); (Z.U.-H.)
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Han Y, Wang Z, Ren J, Wei Z, Li J. Potential inhibitors for the novel coronavirus (SARS-CoV-2). Brief Bioinform 2021; 22:1225-1231. [PMID: 32942296 PMCID: PMC7543260 DOI: 10.1093/bib/bbaa209] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/27/2020] [Accepted: 08/12/2020] [Indexed: 01/03/2023] Open
Abstract
The lack of a vaccine or any effective treatment for the aggressive novel coronavirus disease (COVID-19) has created a sense of urgency for the discovery of effective drugs. Several repurposing pharmaceutical candidates have been reported or envisaged to inhibit the emerging infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but their binding sites, binding affinities and inhibitory mechanisms are still unavailable. In this study, we use the ligand-protein docking program and molecular dynamic simulation to ab initio investigate the binding mechanism and inhibitory ability of seven clinically approved drugs (Chloroquine, Hydroxychloroquine, Remdesivir, Ritonavir, Beclabuvir, Indinavir and Favipiravir) and a recently designed α-ketoamide inhibitor (13b) at the molecular level. The results suggest that Chloroquine has the strongest binding affinity with 3CL hydrolase (Mpro) among clinically approved drugs, indicating its effective inhibitory ability for SARS-CoV-2. However, the newly designed inhibitor 13b shows potentially improved inhibition efficiency with larger binding energy compared with Chloroquine. We further calculate the important binding site residues at the active site and demonstrate that the MET 165 and HIE 163 contribute the most for 13b, while the MET 165 and GLN 189 for Chloroquine, based on residual energy decomposition analysis. The proposed work offers a higher research priority for 13b to treat the infection of SARS-CoV-2 and provides theoretical basis for further design of effective drug molecules with stronger inhibition.
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Affiliation(s)
| | | | - Jiahao Ren
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine
| | - Zhiyun Wei
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication; Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano Electronics, Shanghai Jiao Tong University
| | - Jinjin Li
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Shanghai Jiao Tong University, Shanghai, 200240, China
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Zou T, Huang Y, Hu Y, Wu M, Zhao Y, Du F, Li M, Wu X, Ji H, Kaboli PJ, Wang S, Xiao Z, Wu Z. Study on the Anti-Tumor Mechanism and Target of Triptolide based on Network Pharmacology and Molecular Docking. Recent Pat Anticancer Drug Discov 2021; 16:426-435. [PMID: 33573560 DOI: 10.2174/1574892816666210211143059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/30/2020] [Accepted: 12/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND According to the special physiological and pharmacological activities of natural compounds, many drugs with special therapeutic effects have been developed. The triptolide (TP) is a kind of natural anti-tumor drug with a world patent, but its target and mechanism are yet not known. OBJECTIVE The study aims to explore and predict the target and mechanism of TP on non-small cell lung cancer (NSCLC), pancreatic cancer (PC) and colorectal cancer (CC) through network pharmacology technology. METHODS We screened the core targets of TP with NSCLC, PC and CC, respectively, and carried out network analysis, enrichment analysis and ligand-receptor docking to clarify its potential pharmacological mechanism. RESULTS By screening the core genes between TP with NSCLC, PC and CC, respectively, it was found that PTGS2 was the common target gene in the three cancers. NSCLC, CCL2, IL6, HMOX1 and COL1A1 are the specific target genes, while MMP2, JUN, and CXCL8 are the specific target genes in PC. In CC, the specific target genes includeERBB2, VEGFA, STAT1 andMAPK8. In enrichment analysis, it was found that the NF- κB, toll-like receptors and IL-17 signaling pathway were mainly involved in TP for these cancers. The binding energy of TP to the core target is less than that of cyclophosphamide. CONCLUSIONS This study preliminarily revealed that TP may prevent and treat cancers\ through multiple targets and pathways. The possible mechanisms of TP include regulating immune and inflammatory responses, promoting apoptosis and inhibiting tumor development. It shows that TP may have a potential in treating kinds of tumors.
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Affiliation(s)
- Tao Zou
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000. China
| | - Yuanqiong Huang
- Department of Nephropathy, Luzhou Traditional Chinese Medicine Hospital, Luzhou 646000. China
| | - Yifan Hu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000. China
| | - Mingyu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000. China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000. China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000. China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000. China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000. China
| | - Huijiao Ji
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000. China
| | - Parham Jabbarzadeh Kaboli
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000. China
| | - Shurong Wang
- Department of Pharmacy, the Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China;, Luzhou 646000. China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000. China
| | - Zhigui Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000. China
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Wu Y, Lou L, Xie ZR. A Pilot Study of All-Computational Drug Design Protocol-From Structure Prediction to Interaction Analysis. Front Chem 2020; 8:81. [PMID: 32117898 PMCID: PMC7028743 DOI: 10.3389/fchem.2020.00081] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/24/2020] [Indexed: 11/13/2022] Open
Abstract
Speeding up the drug discovery process is of great significance. To achieve that, high-efficiency methods should be exploited. The conventional wet-bench methods hardly meet the high-speed demand due to time-consuming experiments. Conversely, in silico approaches are much more efficient for drug discovery and design. However, in silico approaches usually serve as a supportive role in research processes. To fully exert the strength of computational methods, we propose a protocol which integrates various in silico approaches, from de novo protein structure prediction to ligand-protein interaction simulation. As a proof of concept, human SK2/calmodulin complex was used as a target for validation. First, we obtained a predicted structure of SK2/calmodulin and predicted binding sites which were consistent with the literature data. Then we investigated the ligand-protein interaction via virtual mutagenesis, flexible docking, and binding affinity calculation. As a result, the binding energies of mutants have similar trends compared with the EC50 values (R = 0.6 for NS309 in V481 mutants). The results indicate that our protocol can be applied to the drug design of structure unknown proteins. Our study also demonstrates that the integration of in silico approaches is feasible and it facilitates the acceleration of new drug discovery.
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Affiliation(s)
- Yifei Wu
- Computational Drug Discovery Laboratory, School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens, GA, United States
| | - Lei Lou
- Computational Drug Discovery Laboratory, School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens, GA, United States
| | - Zhong-Ru Xie
- Computational Drug Discovery Laboratory, School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens, GA, United States
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